| pubmed-article:20056654 | rdf:type | pubmed:Citation | lld:pubmed |
| pubmed-article:20056654 | lifeskim:mentions | umls-concept:C1511790 | lld:lifeskim |
| pubmed-article:20056654 | lifeskim:mentions | umls-concept:C1511726 | lld:lifeskim |
| pubmed-article:20056654 | lifeskim:mentions | umls-concept:C0005456 | lld:lifeskim |
| pubmed-article:20056654 | lifeskim:mentions | umls-concept:C1149367 | lld:lifeskim |
| pubmed-article:20056654 | pubmed:issue | 7 | lld:pubmed |
| pubmed-article:20056654 | pubmed:dateCreated | 2010-4-13 | lld:pubmed |
| pubmed-article:20056654 | pubmed:abstractText | Coupling chromatin immunoprecipitation (ChIP) with recently developed massively parallel sequencing technologies has enabled genome-wide detection of protein-DNA interactions with unprecedented sensitivity and specificity. This new technology, ChIP-Seq, presents opportunities for in-depth analysis of transcription regulation. In this study, we explore the value of using ChIP-Seq data to better detect and refine transcription factor binding sites (TFBS). We introduce a novel computational algorithm named Hybrid Motif Sampler (HMS), specifically designed for TFBS motif discovery in ChIP-Seq data. We propose a Bayesian model that incorporates sequencing depth information to aid motif identification. Our model also allows intra-motif dependency to describe more accurately the underlying motif pattern. Our algorithm combines stochastic sampling and deterministic 'greedy' search steps into a novel hybrid iterative scheme. This combination accelerates the computation process. Simulation studies demonstrate favorable performance of HMS compared to other existing methods. When applying HMS to real ChIP-Seq datasets, we find that (i) the accuracy of existing TFBS motif patterns can be significantly improved; and (ii) there is significant intra-motif dependency inside all the TFBS motifs we tested; modeling these dependencies further improves the accuracy of these TFBS motif patterns. These findings may offer new biological insights into the mechanisms of transcription factor regulation. | lld:pubmed |
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| pubmed-article:20056654 | pubmed:language | eng | lld:pubmed |
| pubmed-article:20056654 | pubmed:journal | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:20056654 | pubmed:citationSubset | IM | lld:pubmed |
| pubmed-article:20056654 | pubmed:chemical | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:20056654 | pubmed:status | MEDLINE | lld:pubmed |
| pubmed-article:20056654 | pubmed:month | Apr | lld:pubmed |
| pubmed-article:20056654 | pubmed:issn | 1362-4962 | lld:pubmed |
| pubmed-article:20056654 | pubmed:author | pubmed-author:ChinnaiyanAru... | lld:pubmed |
| pubmed-article:20056654 | pubmed:author | pubmed-author:QinZhaohui... | lld:pubmed |
| pubmed-article:20056654 | pubmed:author | pubmed-author:YuJindanJ | lld:pubmed |
| pubmed-article:20056654 | pubmed:author | pubmed-author:TaylorJeremy... | lld:pubmed |
| pubmed-article:20056654 | pubmed:author | pubmed-author:HuMingM | lld:pubmed |
| pubmed-article:20056654 | pubmed:issnType | Electronic | lld:pubmed |
| pubmed-article:20056654 | pubmed:volume | 38 | lld:pubmed |
| pubmed-article:20056654 | pubmed:owner | NLM | lld:pubmed |
| pubmed-article:20056654 | pubmed:authorsComplete | Y | lld:pubmed |
| pubmed-article:20056654 | pubmed:pagination | 2154-67 | lld:pubmed |
| pubmed-article:20056654 | pubmed:dateRevised | 2011-8-1 | lld:pubmed |
| pubmed-article:20056654 | pubmed:meshHeading | pubmed-meshheading:20056654... | lld:pubmed |
| pubmed-article:20056654 | pubmed:meshHeading | pubmed-meshheading:20056654... | lld:pubmed |
| pubmed-article:20056654 | pubmed:meshHeading | pubmed-meshheading:20056654... | lld:pubmed |
| pubmed-article:20056654 | pubmed:meshHeading | pubmed-meshheading:20056654... | lld:pubmed |
| pubmed-article:20056654 | pubmed:meshHeading | pubmed-meshheading:20056654... | lld:pubmed |
| pubmed-article:20056654 | pubmed:meshHeading | pubmed-meshheading:20056654... | lld:pubmed |
| pubmed-article:20056654 | pubmed:meshHeading | pubmed-meshheading:20056654... | lld:pubmed |
| pubmed-article:20056654 | pubmed:meshHeading | pubmed-meshheading:20056654... | lld:pubmed |
| pubmed-article:20056654 | pubmed:meshHeading | pubmed-meshheading:20056654... | lld:pubmed |
| pubmed-article:20056654 | pubmed:year | 2010 | lld:pubmed |
| pubmed-article:20056654 | pubmed:articleTitle | On the detection and refinement of transcription factor binding sites using ChIP-Seq data. | lld:pubmed |
| pubmed-article:20056654 | pubmed:affiliation | Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA. | lld:pubmed |
| pubmed-article:20056654 | pubmed:publicationType | Journal Article | lld:pubmed |
| pubmed-article:20056654 | pubmed:publicationType | Research Support, U.S. Gov't, Non-P.H.S. | lld:pubmed |
| pubmed-article:20056654 | pubmed:publicationType | Research Support, Non-U.S. Gov't | lld:pubmed |
| pubmed-article:20056654 | pubmed:publicationType | Evaluation Studies | lld:pubmed |
| pubmed-article:20056654 | pubmed:publicationType | Research Support, N.I.H., Extramural | lld:pubmed |
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